Gene description for CDK9
Gene name cyclin-dependent kinase 9
Gene symbol CDK9
Other names/aliases C-2k
CDC2L4
CTK1
PITALRE
TAK
Species Homo sapiens
 Database cross references - CDK9
ExoCarta ExoCarta_1025
Vesiclepedia VP_1025
Entrez Gene 1025
HGNC 1780
MIM 603251
UniProt P50750  
 CDK9 identified in exosomes derived from the following tissue/cell type
Gastric cancer cells 33991177    
Gastric cancer cells 33991177    
Gastric cancer cells 33991177    
Mesenchymal stem cells 36408942    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Thymus 23844026    
 Gene ontology annotations for CDK9
Molecular Function
    DNA binding GO:0003677 IDA
    protein kinase activity GO:0004672 TAS
    cyclin-dependent protein serine/threonine kinase activity GO:0004693 IEA
    transcription regulatory region DNA binding GO:0044212 IEA
    chromatin binding GO:0003682 IEA
    ATP binding GO:0005524 IEA
    protein binding GO:0005515 IPI
    snRNA binding GO:0017069 IEA
    RNA polymerase II carboxy-terminal domain kinase activity GO:0008353 IDA
Biological Process
    positive regulation of mRNA 3'-UTR binding GO:1903839 IDA
    gene expression GO:0010467 TAS
    regulation of mitotic cell cycle GO:0007346 IMP
    positive regulation of viral transcription GO:0050434 TAS
    positive regulation of histone phosphorylation GO:0033129 IMP
    transcription from RNA polymerase II promoter GO:0006366 TAS
    transcription elongation from RNA polymerase II promoter GO:0006368 TAS
    positive regulation of histone H2B ubiquitination GO:2001168 IMP
    transcription, DNA-templated GO:0006351 TAS
    transcription initiation from RNA polymerase II promoter GO:0006367 TAS
    negative regulation of cell cycle arrest GO:0071157 IDA
    DNA repair GO:0006281 IEA
    cellular response to cytokine stimulus GO:0071345 IDA
    cell proliferation GO:0008283 TAS
    transforming growth factor beta receptor signaling pathway GO:0007179 TAS
    regulation of DNA repair GO:0006282 IDA
    positive regulation of transcription from RNA polymerase II promoter GO:0045944 TAS
    replication fork arrest GO:0043111 IDA
    protein phosphorylation GO:0006468 IDA
    regulation of histone modification GO:0031056 IDA
    negative regulation of mRNA polyadenylation GO:1900364 IMP
    viral process GO:0016032 TAS
Subcellular Localization
    transcription elongation factor complex GO:0008023 IDA
    membrane GO:0016020 IDA
    intracellular membrane-bounded organelle GO:0043231 IDA
    nucleoplasm GO:0005654 TAS
    cytoplasm GO:0005737 IEA
    positive transcription elongation factor complex b GO:0008024 IDA
    PML body GO:0016605 IDA
 Experiment description of studies that identified CDK9 in exosomes
1
Experiment ID 363
ISEV standards
✘ EV Biophysical techniques
✔
TSG101|GAPDH|AQP1|CD151|CD81|CD82|CD9|EPCAM|FLOT1|FLOT2|ICAM1|ITGA2B|LAMP2|RAB35|RAB5A|RAB5B|SDCBP|TFRC|UCHL1
EV Enriched markers
✔
DCLK1
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 33991177    
Organism Homo sapiens
Experiment description Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells
Authors Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M.
Journal name Proteomics
Publication year 2021
Sample Gastric cancer cells
Sample name MKN1 - 100K pellet
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
2
Experiment ID 364
ISEV standards
✘ EV Biophysical techniques
✔
TSG101|GAPDH|AQP1|CD151|CD81|CD82|CD9|EPCAM|FLOT1|FLOT2|ICAM1|ITGA2B|LAMP2|RAB35|RAB5A|RAB5B|SDCBP|TFRC|UCHL1
EV Enriched markers
✔
DCLK1
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 33991177    
Organism Homo sapiens
Experiment description Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells
Authors Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M.
Journal name Proteomics
Publication year 2021
Sample Gastric cancer cells
Sample name MKN1 - 100K pellet
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
3
Experiment ID 365
ISEV standards
✘ EV Biophysical techniques
✔
TSG101|GAPDH|AQP1|CD151|CD81|CD82|CD9|EPCAM|FLOT1|FLOT2|ICAM1|ITGA2B|LAMP2|RAB35|RAB5A|RAB5B|SDCBP|TFRC|UCHL1
EV Enriched markers
✔
DCLK1
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 33991177    
Organism Homo sapiens
Experiment description Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells
Authors Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M.
Journal name Proteomics
Publication year 2021
Sample Gastric cancer cells
Sample name MKN1 - 100K pellet
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
4
Experiment ID 488
ISEV standards
✔
EM
EV Biophysical techniques
✔
CD9|CD81|CD63|GAPDH|SDCBP|LAMP1|TFRC|UCHL1|FLOT2|LAMP2|FLOT1|ICAM1|RAB5B|CD151|RAB35|TSG101|RAB5A|CD82
EV Enriched markers
✔
CANX
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Homo sapiens
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Mesenchymal stem cells
Sample name UCMSC
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
5
Experiment ID 211
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|Alix|EpCAM|TFRC
EV Enriched markers
✔
cytochrome c|GOLGA2
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name IGROV1
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
6
Experiment ID 212
ISEV standards
✔
CEM
EV Biophysical techniques
✔
TSG101|Alix|EpCAM|TFRC
EV Enriched markers
✔
Cytochrome C|GOLGA2
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name OVCAR-3
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
7
Experiment ID 217
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|CD81|CD9|CD63
EV Enriched markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23844026    
Organism Homo sapiens
Experiment description Characterization of human thymic exosomes.
Authors Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O.
Journal name PLoS One
Publication year 2013
Sample Thymus
Sample name Normal-Thymus
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for CDK9
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 CCNT2  
Invivo Homo sapiens
2 MYBL2 4605
Invitro Homo sapiens
Invivo Homo sapiens
3 HTATSF1 27336
Invitro Homo sapiens
Invivo Homo sapiens
4 MDFIC 29969
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
5 RELA 5970
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
6 CDC34 997
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
7 HEXIM1 10614
Affinity Capture-Western Homo sapiens
8 CCNK  
Invivo Homo sapiens
Invitro Homo sapiens
Two-hybrid Homo sapiens
9 AR 367
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
10 SKP1 6500
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
11 GRN 2896
Affinity Capture-Western Homo sapiens
12 SKP2  
Affinity Capture-Western Homo sapiens
13 TRAF2 7186
Invivo Homo sapiens
Two-hybrid Homo sapiens
14 CUL1 8454
Affinity Capture-Western Homo sapiens
15 MYC  
Affinity Capture-Western Homo sapiens
16 AFF4 27125
Affinity Capture-Western Homo sapiens
17 RB1 5925
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
18 NUFIP1  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
19 IL6ST 3572
Reconstituted Complex Homo sapiens
20 CCNT1  
Reconstituted Complex Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Invivo Homo sapiens
Invivo Homo sapiens
Invitro Homo sapiens
Invitro Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
21 HSPA1A 3303
Invivo Homo sapiens
Invitro Homo sapiens
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